The ability for a user to enter custom text for the user interface tool tips (similar to the SimpleViewer languageList configuration option) is on the roadmap and will hopefully be introduced in a future version of Juicebox-Pro. However, I do not know when this may be.
Unfortunately, in the meantime, we are unable to provide customized versions of the 'juicebox.js' JavaScript file.

There may be a conflict between the CSS of your current WordPress theme and the CSS of the Juicebox-Pro gallery itself.
If there are any generalized CSS rules within the theme which apply, for example, to all divs or all images on the web page, then they will also apply to all divs or all images within the Juicebox-Pro gallery on the web page.
If possible, ensure that CSS rules are applied to only those elements on your web page that require them through use of classes and ids.

Try temporarily reverting to the default WordPress theme to see if this makes a difference.

If there is a CSS conflict, one way to isolate a Juicebox gallery from the rest of your web page is to embed the gallery in an iframe, documented as Option #2 here.

Viewing the gallery on its own web page by visiting http://yoojin.star-bottle.net/juicebox_ … index.html in IE9 displays the captions OK so this implies that the problem may lie with the web page into which the gallery is being embedded.

There is no Doctype Declaration on the page into which the gallery is being embedded via an iframe: http://yoojin.star-bottle.net/art.html
Try adding a Doctype Declaration to this web page to see if it helps.

Also, you can validate your web pages using the W3C Markup Validation Service and fix any errors reported. There are several errors on the http://yoojin.star-bottle.net/art.html page, such as

Once the code on your web pages validates OK, your web pages should be rendered with greater predictability and consistency across different browsers.

Juicebox-Pro does not feature any built-in lightbox functionality but it is possible to display a Juicebox gallery in a lightbox such as Shadowbox.
(1) Create a Juicebox gallery with the method of your choice (such as JuiceboxBuilder-Pro).
(2) Upload the complete gallery folder (not just the contents) to your web server.
(3) Include the required Shadowbox files and code on your web page:

<link rel="stylesheet" type="text/css" href="shadowbox.css">
<script type="text/javascript" src="shadowbox.js"></script>
<script type="text/javascript">
Shadowbox.init();
</script>

(4) Create a link on your web page to point to your Juicebox gallery's 'index.html' page, setting the 'rel' attribute to 'shadowbox', such as the following:

<a href="http://www.example.com/gallery/index.html" rel="shadowbox">Open Gallery</a>

As far as I am aware, no. Juicebox-Pro will display the titles and captions exactly as they are in the gallery's XML file.
However, WP-Juicebox and qTranslate are both free so you can try it for yourself to check before purchasing Juicebox-Pro.
WP-Juicebox can be downloaded from this web page.

If you found a plugin which conflicts with WP-Juicebox, please let me know what the plugin is so that I can investigate further and fix the problem for the next version of WP-Juicebox.
If the problem was the BulletProof Security plugin or a similar plugin, it may just need to be configured correctly to work with WP-Juicebox.

It looks like your WordPress installation is inserting <p> and <br /> tags in your embedding code which is adding extra space between the text 'Cakes' and the top of the gallery.
If you look at the source of your web page, your gallery's embedding code looks like this:

<p><!--START JUICEBOX EMBED--><br />
<script src="http://www.clairscakes.com/gallery2/cakes/jbcore/juicebox.js"></script><br />
<script>
  new juicebox({
      containerId : 'juicebox-container',
      baseUrl : 'http://www.clairscakes.com/gallery2/cakes/',
  });
  </script></p>
<div id="juicebox-container"></div>
<p><!--END JUICEBOX EMBED--></p>

... whereas, it should look like the code in your original post.

When entering the embedding code, make sure that the method of entry is 'HTML' rather than 'Visual'.
If that does not help, try temporarily reverting to the default WordPress theme to see if your current WordPress theme is the cause of the extra HTML tags.

You should be able to embed a Juicebox gallery by using either the baseUrl or iframe method documented here.
If you are unsure as to what the relative paths should be within your gallery's embedding code (which can be difficult to figure out in a CMS environment), try using absolute paths instead, e.g.:

<!--START JUICEBOX EMBED-->
<script src="http://www.example.com/my_gallery_folder/jbcore/juicebox.js"></script>
<script>
  new juicebox({
      containerId : 'juicebox-container',
      baseUrl : 'http://www.example.com/my_gallery_folder/',
  });
  </script>
<div id="juicebox-container"></div>
<!--END JUICEBOX EMBED-->

... or:

<iframe src="http://www.example.com/my_gallery_folder/index.html" width="800" height="600" frameborder="0" scrolling="no"></iframe>

I am not sure exactly what you are trying to do but you can style captions using HTML tags within the captions themselves.
For example, you could enter a caption such as the following into an image's caption field in the 'Images' tab of JuiceboxBuilder-Pro to achieve a multi-line caption with different indentations for each line.

<span style="margin: 20px;">Line 1</span><br /><span style="margin: 40px;">Line 2</span>

There are also configuration options available (such as maxCaptionHeight) which might help with your scenario (depending on where in your gallery your captions are positioned).

Otherwise, if you wish to modify the 'jbcore/classic/theme.css' file, the section which deals with the gallery caption area can be found starting at line 193 of the Juicebox-Pro v1.2.0 version.

Having set all the margin and padding options in the 'jbcore/classic/theme.css' to zero with no difference in the gap you describe, it looks like this margin of 10px is hardcoded in the 'jbcore/juicebox.js' file and as this file is obfuscated, it cannot be modified.
Please see this FAQ: Does Juicebox-Pro include the source code?

JuiceboxBuilder-Pro does not retain IPTC (or EXIF) data from the original images when generating new resized images.
A workaround would be to resize your images in Photoshop prior to feeding them to JuiceboxBuilder-Pro and deselect the 'Resize Images' checkbox (in the 'Image Size' control panel on the 'Images' tab) so that JuiceboxBuilder-Pro simply copies your images across into the gallery's 'images' folder, complete with the embedded meta data.

Make sure that you are using the latest versions of both Adobe Air (v3.5) and JuiceboxBuilder-Lite (v1.2.0).
The latest version of Adobe Air can be downloaded from this web page.
Please see the Upgrading Juicebox web page for instructions on how to download and install the latest version of JuiceboxBuilder-Lite.

If this does not help, try manually deleting the following folder:

• Mac: /Users/your_username/Library/Application Support/Adobe/AIR/ELS/JuiceboxBuilder-Lite

• Windows (XP): C:\Documents and Settings\your_username\Application Data\Adobe\AIR\ELS\JuiceboxBuilder-Lite

• Windows (Vista, Win 7): C:\Users\your_username\AppData\Roaming\Adobe\AIR\ELS\JuiceboxBuilder-Lite

It looks like the bottom of your Juicebox gallery is being obscured by the 'footer3' div on your web page (and the second row of thumbnails is being displayed by Juicebox but is hidden from view).
Check the CSS heights of all containers on your web page and make sure that everything add up correctly to see if this helps solve your problem.